Document Type
Article
Publication Date
1-1-2023
Original Citation
Danis D,
Jacobsen J,
Wagner A,
Groza T,
Beckwith M,
Rekerle L,
Carmody L,
Reese J,
Hegde H,
Ladewig M,
Seitz B,
Munoz-Torres M,
Harris N,
Rambla J,
Baudis M,
Mungall C,
Haendel M,
Robinson P.
Phenopacket-tools: Building and validating GA4GH Phenopackets. PLoS One. 2023;18(5):e0285433.
Keywords
JGM, Humans, Software, Genomics, Databases, Factual, Neoplasms, Gene Library
JAX Source
PLoS One. 2023;18(5):e0285433.
ISSN
1932-6203
PMID
37196000
DOI
https://doi.org/10.1371/journal.pone.0285433
Grant
This work was supported by the National Institutes of Health (NIH) under NIH NHGRI RM1HG010860, NIH NHGRI 1R01HG011799-01, NIH OD R24OD011883, NIH NICHD 1R01HD103805-01, NIH NLM contract #75N97019P00280. JR, HH, NLH and CJM were supported in part by Director, Office of Science, Office of Basic Energy Sciences of the U.S.
Abstract
The Global Alliance for Genomics and Health (GA4GH) is a standards-setting organization that is developing a suite of coordinated standards for genomics. The GA4GH Phenopacket Schema is a standard for sharing disease and phenotype information that characterizes an individual person or biosample. The Phenopacket Schema is flexible and can represent clinical data for any kind of human disease including rare disease, complex disease, and cancer. It also allows consortia or databases to apply additional constraints to ensure uniform data collection for specific goals. We present phenopacket-tools, an open-source Java library and command-line application for construction, conversion, and validation of phenopackets. Phenopacket-tools simplifies construction of phenopackets by providing concise builders, programmatic shortcuts, and predefined building blocks (ontology classes) for concepts such as anatomical organs, age of onset, biospecimen type, and clinical modifiers. Phenopacket-tools can be used to validate the syntax and semantics of phenopackets as well as to assess adherence to additional user-defined requirements. The documentation includes examples showing how to use the Java library and the command-line tool to create and validate phenopackets. We demonstrate how to create, convert, and validate phenopackets using the library or the command-line application. Source code, API documentation, comprehensive user guide and a tutorial can be found at https://github.com/phenopackets/phenopacket-tools. The library can be installed from the public Maven Central artifact repository and the application is available as a standalone archive. The phenopacket-tools library helps developers implement and standardize the collection and exchange of phenotypic and other clinical data for use in phenotype-driven genomic diagnostics, translational research, and precision medicine applications.
Comments
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.